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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 22-36875840-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=36875840&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 36875840,
"ref": "T",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000248899.11",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "c.815T>C",
"hgvs_p": "p.Leu272Pro",
"transcript": "ENST00000397147.7",
"protein_id": "ENSP00000380334.4",
"transcript_support_level": 1,
"aa_start": 272,
"aa_end": null,
"aa_length": 348,
"cds_start": 815,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 999,
"cdna_end": null,
"cdna_length": 1643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "c.758+57T>C",
"hgvs_p": null,
"transcript": "NM_000631.5",
"protein_id": "NP_000622.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 339,
"cds_start": -4,
"cds_end": null,
"cds_length": 1020,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1378,
"mane_select": "ENST00000248899.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "c.758+57T>C",
"hgvs_p": null,
"transcript": "ENST00000248899.11",
"protein_id": "ENSP00000248899.6",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 339,
"cds_start": -4,
"cds_end": null,
"cds_length": 1020,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1378,
"mane_select": "NM_000631.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "P",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "c.815T>C",
"hgvs_p": "p.Leu272Pro",
"transcript": "NM_013416.4",
"protein_id": "NP_038202.2",
"transcript_support_level": null,
"aa_start": 272,
"aa_end": null,
"aa_length": 348,
"cds_start": 815,
"cds_end": null,
"cds_length": 1047,
"cdna_start": 981,
"cdna_end": null,
"cdna_length": 1623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "n.405T>C",
"hgvs_p": null,
"transcript": "ENST00000415063.2",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 796,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "c.449+57T>C",
"hgvs_p": null,
"transcript": "ENST00000650698.1",
"protein_id": "ENSP00000498381.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 236,
"cds_start": -4,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "c.449+57T>C",
"hgvs_p": null,
"transcript": "ENST00000650827.1",
"protein_id": "ENSP00000498212.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 236,
"cds_start": -4,
"cds_end": null,
"cds_length": 711,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1260,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "n.1067+53T>C",
"hgvs_p": null,
"transcript": "ENST00000651053.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "c.932+57T>C",
"hgvs_p": null,
"transcript": "XM_047441384.1",
"protein_id": "XP_047297340.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 397,
"cds_start": -4,
"cds_end": null,
"cds_length": 1194,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2184,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "c.902+57T>C",
"hgvs_p": null,
"transcript": "XM_047441385.1",
"protein_id": "XP_047297341.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 387,
"cds_start": -4,
"cds_end": null,
"cds_length": 1164,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1852,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"hgvs_c": "c.*8T>C",
"hgvs_p": null,
"transcript": "ENST00000447071.5",
"protein_id": "ENSP00000414958.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 165,
"cds_start": -4,
"cds_end": null,
"cds_length": 498,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NCF4",
"gene_hgnc_id": 7662,
"dbsnp": "rs2075939",
"frequency_reference_population": 0.83093846,
"hom_count_reference_population": 558514,
"allele_count_reference_population": 1341153,
"gnomad_exomes_af": 0.827791,
"gnomad_genomes_af": 0.86117,
"gnomad_exomes_ac": 1210107,
"gnomad_genomes_ac": 131046,
"gnomad_exomes_homalt": 501774,
"gnomad_genomes_homalt": 56740,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0000011522777185746236,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.124,
"revel_prediction": "Benign",
"alphamissense_score": 0.074,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.298,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000248899.11",
"gene_symbol": "NCF4",
"hgnc_id": 7662,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.758+57T>C",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive, chronic, cytochrome b-positive, type 3,Granulomatous disease,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7 O:1",
"phenotype_combined": "not specified|Granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 3|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}